Genetic and haplotypic structure in 14 European and African cattle breeds

Abstract

To evaluate and compare the extent of LD in cattle, 1536 SNPs, mostly localized on BTA03, were detected in silico from available sequence data using two different methods and genotyped on samples from 14 distinct breeds originating from Europe and Africa. Only 696 SNPs could be validated, confirming the importance of trace-quality information for the in silico detection. Most of the validated SNPs were informative in several breeds and were used for a detailed description of their genetic structure and relationships. Results obtained were in agreement with previous studies performed on microsatellite markers and using larger samples. In addition, the majority of the validated SNPs could be mapped precisely, reaching an average density of one marker every 311 kb. This allowed us to analyze the extent of LD in the different breeds. Decrease of LD with physical distance across breeds revealed footprints of ancestral LD at short distances (<10 kb). As suggested by the haplotype block structure, these ancestral blocks are organized, within a breed, into larger blocks of a few hundred kilobases. In practice, such a structure similar to that already reported in dogs makes it possible to develop a chip of <300,000 SNPs, which should be efficient for mapping purposes in most cattle breeds.

Figure 1.—

Pairwise LD analysis within the different populations and across the corresponding average composite population (30 replicates of a composite population consisting of 56 individuals with 4 randomly drawn within each of the 14 breeds). (A) Number of SNP pairs available for each range of marker distance considered (measured in megabases). (B) Mean r² value for each range of marker distance considered. (C) Estimates of the effective population size (N_e) from r² at different times in the past (measured in number of generations). Further details are given in supplemental Table 3 at http://www.genetics.org/supplemental/.

Figure 2.—

Unrooted consensus tree showing the genetic relationships among the 14 breeds considered using the neighbor-joining method and the unbiased Nei's genetic distance. Numbers at the nodes are the reliabilities in percentages estimated after 10,000 bootstrap resamplings.